Digital economy is a rapidly developing economic form under the background of the information age. This article introduces the construction and optimization of the green supply chain management model of agricultural enterprises under the digital economy, and intends to provide some ideas and directions for the development of green supply chain management of agricultural enterprises based on digital economy. This paper proposes the construction and optimization research methods of the green supply chain management model of agricultural enterprises under the digital economy, including the overview of green supply chain management, the construction of the optimization management model of the green supply chain of agricultural enterprises, and the digital economy under the construction of a green supply chain management practice index system for agricultural enterprises. Experimental results show that average Cronbachα value of each scale factor of the optimized management model in this paper is 0.876, and optimized decision-making coordination mechanism has high internal consistency.